Khan means "ruler" or "commander".
A female khan is called a Khatun or Khanum.
Khagan means 'Khan of Khans' but is often (incorrectly) 'shortened' to Khan. This is similar to how the Persian Shahanshah, 'King of Kings', is usually simply called the Shah. Genghis was also called the 'Great Khan' like how Ottoman Padishah was called the 'Great Sultan'.
Khans rule over Khanates. Khagans rule over Khaganates.
There have been several variations on the title used in modern times. Khan Bahadur or Khan Sahib was a title of honor, granted by India to Muslims who had done major deeds of valor, or service to the nation or government. The Hindu counterpart for this title was Rai Bahadur or Rai Sahib. This title was normally granted in addition to other awards and decorations and added either before or after a person's actual name as a prefix or suffix.
The Mongol empire branched into the Ilkhanate of Persia and the Chagatai Khaganate of Central Asia.